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Hannon-Elledge shRNA Library Standardizes Barcode Technology on Agilent Technologies Microarrays


Gregory Hannon, Ph.D., Howard Hughes Medical Institute investigator at Cold Spring Harbor Laboratory, and Stephen Elledge, Ph.D., pioneers in the construction of short hairpin RNA interference (shRNAi) libraries, have adopted the Agilent Technologies (NYSE: A) microarray platform to read out the individual barcodes present in the libraries and facilitate their screening. The use of the barcode arrays makes it possible, for the first time, for these complex libraries to be used and screened without sophisticated and expensive automation. It represents the democratization of the use of the shRNA libraries, according to Agilent.

RNA interference (RNAi) is a relatively new field of study in which non-coding RNA molecules are used to regulate gene expression and chromatin architecture. The basic mechanisms of RNAi formation and activity provide insight into gene regulation, enable the study of loss of gene activity, and identify and validate pharmaceutical targets. The Hannon-Elledge labs have made seminal contributions to this field by the construction and use of shRNAi libraries for the specific knock-out of all human and mouse genes.

The barcode microarray technology allows researchers to screen pools of shRNAi constructs and decipher the results of cell-based experiments by following up and identifying individual shRNA constructs with the speed provided by microarrays.

The flexibility of the SurePrint ink-jet based in situ probe synthesis, the engine behind the Agilent microarray system, was a significant factor in the decision to adopt this platform, according to Agilent. New content can be added quickly and easily using Agilent’s eArray online microarray design tool, which eliminates design and setup fees. In addition, the introduction of higher densities and multiplexing capacity of the arrays (8 arrays per glass slide), were also factors in the decision to adopt the platform, according to Agilent. The Agilent arrays also provide high signal-to-noise ratios.

“Agilent has been working closely with the Hannon and Elledge labs and is pleased to contribute to the shRNAi screening technology by providing high-quality, high-sensitivity microarrays,” said Leonardo Brizuela, Ph.D., director of science and technology for the Agilent Genomics business unit.

Hannon is the Howard Hughes Medical Institute (HHMI) investigator at Cold Spring Harbor Laboratory. Elledge is the Gregor Mendel Processor of Genetics and HHMI investigator at Harvard Medical School.


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